# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 5069 | 0 | 0.9869 | MC-PRPA-HLFIA Cascade Detection System for Point-of-Care Testing Pan-Drug-Resistant Genes in Urinary Tract Infection Samples. Recently, urinary tract infection (UTI) triggered by bacteria carrying pan-drug-resistant genes, including carbapenem resistance gene bla(NDM) and bla(KPC), colistin resistance gene mcr-1, and tet(X) for tigecycline resistance, have been reported, posing a serious challenge to the treatment of clinical UTI. Therefore, point-of-care (POC) detection of these genes in UTI samples without the need for pre-culturing is urgently needed. Based on PEG 200-enhanced recombinase polymerase amplification (RPA) and a refined Chelex-100 lysis method with HRP-catalyzed lateral flow immunoassay (LFIA), we developed an MCL-PRPA-HLFIA cascade assay system for detecting these genes in UTI samples. The refined Chelex-100 lysis method extracts target DNA from UTI samples in 20 min without high-speed centrifugation or pre-incubation of urine samples. Following optimization, the cascade detection system achieved an LOD of 10(2) CFU/mL with satisfactory specificity and could detect these genes in both simulated and actual UTI samples. It takes less than an hour to complete the process without the use of high-speed centrifuges or other specialized equipment, such as PCR amplifiers. The MCL-PRPA-HLFIA cascade assay system provides new ideas for the construction of rapid detection methods for pan-drug-resistant genes in clinical UTI samples and provides the necessary medication guidance for UTI treatment. | 2023 | 37047757 |
| 9742 | 1 | 0.9864 | BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage. A single, inexpensive diagnostic test capable of rapidly identifying a wide range of genetic biomarkers would prove invaluable in precision medicine. Previous work has demonstrated the potential for high-throughput, label-free detection of A-G-C-T content in DNA k-mers, providing an alternative to single-letter sequencing while also having inherent lossy data compression and massively parallel data acquisition. Here, we apply a new bioinformatics algorithm - block optical content scoring (BOCS) - capable of using the high-throughput content k-mers for rapid, broad-spectrum identification of genetic biomarkers. BOCS uses content-based sequence alignment for probabilistic mapping of k-mer contents to gene sequences within a biomarker database, resulting in a probability ranking of genes on a content score. Simulations of the BOCS algorithm reveal high accuracy for identification of single antibiotic resistance genes, even in the presence of significant sequencing errors (100% accuracy for no sequencing errors, and >90% accuracy for sequencing errors at 20%), and at well below full coverage of the genes. Simulations for detecting multiple resistance genes within a methicillin-resistant Staphylococcus aureus (MRSA) strain showed 100% accuracy at an average gene coverage of merely 0.515, when the k-mer lengths were variable and with 4% sequencing error within the k-mer blocks. Extension of BOCS to cancer and other genetic diseases met or exceeded the results for resistance genes. Combined with a high-throughput content-based sequencing technique, the BOCS algorithm potentiates a test capable of rapid diagnosis and profiling of genetic biomarkers ranging from antibiotic resistance to cancer and other genetic diseases. | 2019 | 31173943 |
| 5068 | 2 | 0.9859 | Ultrasensitive Label-Free Detection of Unamplified Multidrug-Resistance Bacteria Genes with a Bimodal Waveguide Interferometric Biosensor. Infections by multidrug-resistant bacteria are becoming a major healthcare emergence with millions of reported cases every year and an increasing incidence of deaths. An advanced diagnostic platform able to directly detect and identify antimicrobial resistance in a faster way than conventional techniques could help in the adoption of early and accurate therapeutic interventions, limiting the actual negative impact on patient outcomes. With this objective, we have developed a new biosensor methodology using an ultrasensitive nanophotonic bimodal waveguide interferometer (BiMW), which allows a rapid and direct detection, without amplification, of two prevalent and clinically relevant Gram-negative antimicrobial resistance encoding sequences: the extended-spectrum betalactamase-encoding gene blaCTX-M-15 and the carbapenemase-encoding gene blaNDM-5 We demonstrate the extreme sensitivity and specificity of our biosensor methodology for the detection of both gene sequences. Our results show that the BiMW biosensor can be employed as an ultrasensitive (attomolar level) and specific diagnostic tool for rapidly (less than 30 min) identifying drug resistance. The BiMW nanobiosensor holds great promise as a powerful tool for the control and management of healthcare-associated infections by multidrug-resistant bacteria. | 2020 | 33086716 |
| 5072 | 3 | 0.9856 | Integrated Sample to Detection of Carbapenem-Resistant Bacteria Extracted from Water Samples Using a Portable Gold Nanoparticle-Based Biosensor. Antimicrobial resistance (AMR) is a significant global threat and is driven by the overuse of antibiotics in both clinical and agricultural settings. This issue is further complicated by the lack of rapid surveillance tools to detect resistant bacteria in clinical, environmental, and food systems. Of particular concern is the rise in resistance to carbapenems, a critical class of beta-lactam antibiotics. Rapid detection methods are necessary for prevention and surveillance effort. This study utilized a gold nanoparticle-based plasmonic biosensor to detect three CR genes: bla(KPC-3), bla(NDM-1), and bla(OXA-1). Optical signals were analyzed using both a spectrophotometer and a smartphone app that quantified visual color changes using RGB values. This app, combined with a simple boiling method for DNA extraction and a portable thermal cycler, was used to evaluate the biosensor's potential for POC use. Advantages of the portable bacterial detection device include real time monitoring for immediate decision-making in critical situations, field and on-site testing in resource-limited settings without needing to transport samples to a centralized lab, minimal training required, automatic data analysis, storage and sharing, and reduced operational cost. Bacteria were inoculated into sterile water, river water, and turkey rinse water samples to determine the biosensor's success in detecting target genes from sample matrices. Magnetic nanoparticles were used to capture and concentrate bacteria to avoid time-consuming cultivation and separation steps. The biosensor successfully detected the target CR genes in all tested samples using three gene-specific DNA probes. Target genes were detected with a limit of detection of 2.5 ng/L or less, corresponding to ~10(3) CFU/mL of bacteria. | 2025 | 40942723 |
| 5070 | 4 | 0.9856 | Sequence-specific DNA solid-phase extraction in an on-chip monolith: Towards detection of antibiotic resistance genes. Antibiotic resistance of bacteria is a growing problem and presents a challenge for prompt treatment in patients with sepsis. Currently used methods rely on culturing or amplification; however, these steps are either time consuming or suffer from interference issues. A microfluidic device was made from black polypropylene, with a monolithic column modified with a capture oligonucleotide for sequence selective solid-phase extraction of a complementary target from a lysate sample. Porous properties of the monolith allow flow and hybridization of a target complementary to the probe immobilized on the column surface. Good flow-through properties enable extraction of a 100μL sample and elution of target DNA in 12min total time. Using a fluorescently labeled target oligonucleotide related to Verona Integron-Mediated Metallo-β-lactamase it was possible to extract and detect a 1pM sample with 83% recovery. Temperature-mediated elution by heating above the duplex melting point provides a clean extract without any agents that interfere with base pairing, allowing various labeling methods or further downstream processing of the eluent. Further integration of this extraction module with a system for isolation and lysis of bacteria from blood, as well as combining with single-molecule detection should allow rapid determination of antibiotic resistance. | 2017 | 28734608 |
| 5097 | 5 | 0.9856 | Comparing Graph Sample and Aggregation (SAGE) and Graph Attention Networks in the Prediction of Drug-Gene Associations of Extended-Spectrum Beta-Lactamases in Periodontal Infections and Resistance. INTRODUCTION: Gram-negative bacteria exhibit more antibiotic resistance than gram-positive bacteria due to their cell wall structure and composition differences. Porins, or protein channels in these bacteria, can allow small, hydrophilic antibiotics to diffuse, affecting their susceptibility. Mutations in porin protein genes can also impair antibiotic entry. Predicting drug-gene associations of extended-spectrum beta-lactamases (ESBLs) is crucial as they confer resistance to beta-lactam antibiotics, challenging the treatment of infections. This aids clinicians in selecting suitable treatments, optimizing drug usage, enhancing patient outcomes, and controlling antibiotic resistance in healthcare settings. Graph-based neural networks can predict drug-gene associations in periodontal infections and resistance. The aim of the study was to predict drug-gene associations of ESBLs in periodontal infections and resistance. METHODS: The study focuses on analyzing drug-gene associations using probes and drugs. The data was converted into graph language, assigning nodes and edges for drugs and genes. Graph neural networks (GNNs) and similar algorithms were implemented using Google Colab and Python. Cytoscape and CytoHubba are open-source software platforms used for network analysis and visualization. GNNs were used for tasks like node classification, link prediction, and graph-level prediction. Three graph-based models were used: graph convolutional network (GCN), Graph SAGE, and graph attention network (GAT). Each model was trained for 200 epochs using the Adam optimizer with a learning rate of 0.01 and a weight decay of 5e-4. RESULTS: The drug-gene association network has 57 nodes, 79 edges, and a 2.730 characteristic path length. Its structure, organization, and connectivity are analyzed using the GCN and Graph SAGE, which show high accuracy, precision, recall, and an F1-score of 0.94. GAT's performance metrics are lower, with an accuracy of 0.68, precision of 0.47, recall of 0.68, and F1-score of 0.56, suggesting that it may not be as effective in capturing drug-gene relationships. CONCLUSION: Compared to ESBLs, both GCN and Graph SAGE demonstrate excellent performance with accuracy, precision, recall, and an F1-score of 0.94. These results indicate that GCN and Graph SAGE are highly effective in predicting drug-gene associations related to ESBLs. GCN and Graph SAGE outperform GAT in predicting drug-gene associations for ESBLs. Improvements include data augmentation, regularization, and cross-validation. Ethical considerations, fairness, and open-source implementations are crucial for future research in precision periodontal treatment. | 2024 | 39347119 |
| 2497 | 6 | 0.9855 | Rapid Simultaneous Detection of the Clinically Relevant Carbapenemase Resistance Genes blaKPC, blaOXA48, blaVIM and blaNDM with the Newly Developed Ready-to-Use qPCR CarbaScan LyoBead. Antibiotic resistance, in particular the dissemination of carbapenemase-producing organisms, poses a significant threat to global healthcare. This study introduces the qPCR CarbaScan LyoBead assay, a robust, accurate, and efficient tool for detecting key carbapenemase genes, including blaKPC, blaNDM, blaOXA-48, and blaVIM. The assay utilizes lyophilized beads, a technological advancement that enhances stability, simplifies handling, and eliminates the need for refrigeration. This feature renders it particularly well-suited for point-of-care diagnostics and resource-limited settings. The assay's capacity to detect carbapenemase genes directly from bacterial colonies without the need for extensive sample preparation has been demonstrated to streamline workflows and enable rapid diagnostic results. The assay demonstrated 100% specificity and sensitivity across a diverse range of bacterial strains, including multiple allelic variants of target genes, facilitating precise identification of resistance mechanisms. Bacterial strains of the species Acinetobacter baumannii, Citrobacter freundii, Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae and Pseudomonas aeruginosa were utilized as reference material for assay development (n = 9) and validation (n = 28). It is notable that the assay's long shelf life and minimal operational complexity further enhance its utility for large-scale implementation in healthcare, food safety, and environmental monitoring. The findings emphasize the necessity of continuous surveillance and the implementation of rapid diagnostic methods for the effective detection of resistance genes. Furthermore, the assay's potential applications in other fields, such as toxin-antitoxin system research and monitoring of resistant bacteria in the community, highlight its versatility. In conclusion, the qPCR CarbaScan LyoBead assay is a valuable tool that can contribute to the urgent need to combat antibiotic resistance and improve global public health outcomes. | 2025 | 39940986 |
| 5826 | 7 | 0.9855 | Rapid and accurate sepsis diagnostics via a novel probe-based multiplex real-time PCR system. Sepsis is a critical clinical emergency that requires prompt diagnosis and intervention. Its prevalence has increased due to the aging population and increased antibiotic resistance. Early identification and the use of innovative technologies are crucial for improving patient outcomes. Modern methodologies are needed to minimize the turnaround time for diagnosis and improve outcomes. Rapid diagnostic tests and multiplex PCR are effective but have limitations in identifying a range of pathogens and target genes. Our study evaluated two novel probe-based multiplex real-time PCR systems: the SEPSI ID and SEPSI DR panels. These systems can quickly identify bacterial and fungal pathogens, alongside antibiotic resistance genes. The assays cover 29 microorganisms (gram-negative bacteria, gram-positive bacteria, yeast, and mold species), alongside 23 resistance genes and four virulence factors. A streamlined workflow uses 2 µL of broth from positive blood cultures (BCs) without nucleic acid extraction and provides results in approximately 1 h. We present the results from an evaluation of 228 BCs and 22 isolates previously characterized by whole-genome sequencing. In comparison to the reference methods, the SEPSI ID panel demonstrated a sensitivity of 96.88%, a specificity of 100%, and a PPV of 100%, whereas the SEPSI DR panel showed a sensitivity of 97.8%, a PPV of 89.7%, and a specificity of 96.7%. Both panels also identified additional pathogens and resistance-related targets not detected by conventional methods. This assay shows promise for rapidly and accurately diagnosing sepsis. Future studies should validate its performance in various clinical settings to enhance sepsis management and improve patient outcomes.IMPORTANCEWe present a new diagnostic method that enables the quick and precise identification of pathogens and resistance genes from positive blood cultures, eliminating the need for nucleic acid extraction. This technique can also be used on fresh pathogen cultures. It has the potential to greatly improve treatment protocols, leading to better patient outcomes, more responsible antibiotic use, and more efficient management of healthcare resources. | 2025 | 41025980 |
| 2224 | 8 | 0.9855 | Multiplexed Signal Ion Emission Reactive Release Amplification (SIERRA) Assay for the Culture-Free Detection of Gram-Negative and Gram-Positive Bacteria and Antimicrobial Resistance Genes. The global prevalence of antibiotic-resistant bacteria has increased the risk of dangerous infections, requiring rapid diagnosis and treatment. The standard method for diagnosis of bacterial infections remains dependent on slow culture-based methods, carried out in central laboratories, not easily extensible to rapid identification of organisms, and thus not optimal for timely treatments at the point-of-care (POC). Here, we demonstrate rapid detection of bacteria by combining electrochemical immunoassays (EC-IA) for pathogen identification with confirmatory quantitative mass spectral immunoassays (MS-IA) based on signal ion emission reactive release amplification (SIERRA) nanoparticles with unique mass labels. This diagnostic method uses compatible reagents for all involved assays and standard fluidics for automatic sample preparation at POC. EC-IA, based on alkaline phosphatase-conjugated pathogen-specific antibodies, quantified down to 10(4) bacteria per sample when testing Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa lysates. EC-IA quantitation was also obtained for wound samples. The MS-IA using nanoparticles against S. aureus, E. coli, Klebsiella pneumoniae, and P. aeruginosa allowed selective quantitation of ∼10(5) bacteria per sample. This method preserves bacterial cells allowing extraction and amplification of 16S ribosomal RNA genes and antibiotic resistance genes, as was demonstrated through identification and quantitation of two strains of E. coli, resistant and nonresistant due to β-lactamase cefotaximase genes. Finally, the combined immunoassays were compared against culture using remnant deidentified patient urine samples. The sensitivities for these immunoassays were 83, 95, and 92% for the prediction of S. aureus, P. aeruginosa, and E. coli or K. pneumoniae positive culture, respectively, while specificities were 85, 92, and 97%. The diagnostic platform presented here with fluidics and combined immunoassays allows for pathogen isolation within 5 min and identification in as little as 15 min to 1 h, to help guide the decision for additional testing, optimally only on positive samples, such as multiplexed or resistance gene assays (6 h). | 2021 | 33819029 |
| 8432 | 9 | 0.9853 | A 0D-2D Heterojunction Bismuth Molybdate-Anchored Multifunctional Hydrogel for Highly Efficient Eradication of Drug-Resistant Bacteria. Due to the increasing antibiotic resistance and the lack of broad-spectrum antibiotics, there is an urgent requirement to develop fresh strategies to combat multidrug-resistant pathogens. Herein, defect-rich bismuth molybdate heterojunctions [zero-dimensional (0D) Bi(4)MoO(9)/two-dimensional (2D) Bi(2)MoO(6), MBO] were designed for rapid capture of bacteria and synergistic photocatalytic sterilization. The as-prepared MBO was experimentally and theoretically demonstrated to possess defects, heterojunctions, and irradiation triple-enhanced photocatalytic activity for efficient generation of reactive oxygen species (ROS) due to the exposure of more active sites and separation of effective electron-hole pairs. Meanwhile, dopamine-modified MBO (pMBO) achieved a positively charged and rough surface, which conferred strong bacterial adhesion and physical penetration to the nanosheets, effectively trapping bacteria within the damage range and enhancing ROS damage. Based on this potent antibacterial ability of pMBO, a multifunctional hydrogel consisting of poly(vinyl alcohol) cross-linked tannic acid-coated cellulose nanocrystals (CPTB) and pMBO, namely CPTB@pMBO, is developed and convincingly effective against methicillin-resistant Staphylococcus aureus in a mouse skin infection model. In addition, the strategy of combining a failed beta-lactam antibiotic with CPTB@pMBO to photoinactivation with no resistance observed was developed, which presented an idea to address the issue of antibiotic resistance in bacteria and to explore facile anti-infection methods. In addition, CPTB@pMBO can reduce excessive proteolysis of tissue and inflammatory response by regulating the expression of genes and pro-inflammatory factors in vivo, holding great potential for the effective treatment of wound infections caused by drug-resistant bacteria. | 2023 | 37531599 |
| 5073 | 10 | 0.9852 | Parallel Detection of the Unamplified Carbapenem Resistance Genes bla(NDM-1) and bla(OXA-1) Using a Plasmonic Nano-Biosensor with a Field-Portable DNA Extraction Method. Antimicrobial resistance (AMR) is a rapidly growing global concern resulting from the overuse of antibiotics in agricultural and clinical settings. The challenge is exacerbated by the lack of rapid surveillance for resistant bacteria in clinical, environmental, and food supply settings. The increasing resistance to carbapenems, an important sub-class of beta-lactam antibiotics, is a major concern in the healthcare community. Carbapenem resistance (CR) has been found in the environment and food supply chain, where it has the potential to spread to pathogens, animals, and humans through direct or indirect contact. Rapid detection for preventative and control measures should be developed. This study utilized a gold nanoparticle-based plasmonic biosensor for the parallel detection of the CR genes bla(NDM-1) and bla(OXA-1). To explore the field portability, DNA was extracted using two methods: a commercial extraction kit and a boiling method. The results were compared between the two methods using a spectrophotometer and a cellphone application for RGB values to quantify the visual results. The results showed that the boiling method of extraction was more effective than extraction with a commercial kit for this analysis. The parallel detection of unamplified genes extracted via the boiling method is novel. When combined with other portable testing equipment, the approach has the potential to be an inexpensive, rapid, and simple on-site CR gene detection protocol. | 2025 | 39997014 |
| 9741 | 11 | 0.9852 | ARGai 1.0: A GAN augmented in silico approach for identifying resistant genes and strains in E. coli using vision transformer. The emergence of infectious disease and antibiotic resistance in bacteria like Escherichia coli (E. coli) shows the necessity for novel computational techniques for identifying essential genes that contribute to resistance. The task of identifying resistant strains and multi-drug patterns in E. coli is a major challenge with whole genome sequencing (WGS) and next-generation sequencing (NGS) data. To address this issue, we suggest ARGai 1.0 a deep learning architecture enhanced with generative adversarial networks (GANs). We mitigate data scarcity difficulties by augmenting limited experimental datasets with synthetic data generated by GANs. Our in-silico method (augmentation with feature selection) improves the identification of resistance genes in E. coli by using feature extraction techniques to identify valuable features from actual and GAN-generated data. Employing comprehensive validation, we exhibit the effectiveness of our ARGai 1.0 in precisely identifying the informative and resistant genes. In addition, our ARGai 1.0 identifies the resistant strains with a classification accuracy of 98.96 % on Deep Convolutional Generative Adversarial Network (DCGAN) augmented data. Additionally, ARGai 1.0 achieves more than 98 % of sensitivity and specificity. We also benchmark our ARGai 1.0 with several state-of-the-art AI models for resistant strain classification. In the fight against antibiotic resistance, ARGai 1.0 offers a promising avenue for computational genomics. With implications for research and clinical practice, this work shows the potential of deep networks with GAN augmentation as a practical and successful method for gene identification in E. coli. | 2025 | 39813877 |
| 8184 | 12 | 0.9852 | Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria. The emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. Here we report the development of a series of CRISPR-Cas13a-based antibacterial nucleocapsids, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus by recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs are generated by packaging programmed CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibit strong bacterial killing activities upon recognizing target genes regardless of their location. Moreover, we also demonstrate that the CapsidCas13a(s) can be applied to detect bacterial genes through gene-specific depletion of bacteria without employing nucleic acid manipulation and optical visualization devices. Our data underscore the potential of CapsidCas13a(s) as both therapeutic agents against antimicrobial-resistant bacteria and nonchemical agents for detection of bacterial genes. | 2020 | 32523110 |
| 9995 | 13 | 0.9852 | Direct fluorescence in situ hybridization (FISH) in Escherichia coli with a target-specific quantum dot-based molecular beacon. Quantum dots (QDs) are inorganic fluorescent nanocrystals with excellent properties such as tunable emission spectra and photo-bleaching resistance compared with organic dyes, which make them appropriate for applications in molecular beacons. In this work, quantum dot-based molecular beacons (QD-based MBs) were fabricated to specifically detect β-lactamase genes located in pUC18 which were responsible for antibiotic resistance in bacteria Escherichia coli (E. coli) DH5α. QD-based MBs were constructed by conjugating mercaptoacetic acid-quantum dots (MAA-QDs) with black hole quencher 2 (BHQ2) labeled thiol DNA vial metal-thiol bonds. Two types of molecular beacons, double-strands beacons and hairpin beacons, were observed in product characterization by gel electrophoresis. Using QD-based MBs, one-step FISH in tiny bacteria DH5α was realized for the first time. QD-based MBs retained their bioactivity when hybridizing with complementary target DNA, which showed excellent advantages of eliminating background noise caused by adsorption of non-specific bioprobes and achieving clearer focus of genes in plasmids pUC18, and capability of bacterial cell penetration and signal specificity in one-step in situ hybridization. | 2010 | 20729070 |
| 9743 | 14 | 0.9852 | Simultaneous Detection of Antibiotic Resistance Genes on Paper-Based Chip Using [Ru(phen)(2)dppz](2+) Turn-on Fluorescence Probe. Antibiotic resistance, the ability of some bacteria to resist antibiotic drugs, has been a major global health burden due to the extensive use of antibiotic agents. Antibiotic resistance is encoded via particular genes; hence the specific detection of these genes is necessary for diagnosis and treatment of antibiotic resistant cases. Conventional methods for monitoring antibiotic resistance genes require the sample to be transported to a central laboratory for tedious and sophisticated tests, which is grueling and time-consuming. We developed a paper-based chip, integrated with loop-mediated isothermal amplification (LAMP) and the "light switch" molecule [Ru(phen)(2)dppz](2+), to conduct turn-on fluorescent detection of antibiotic resistance genes. In this assay, the amplification reagents can be embedded into test spots of the chip in advance, thus simplifying the detection procedure. [Ru(phen)(2)dppz](2+) was applied to intercalate into amplicons for product analysis, enabling this assay to be operated in a wash-free format. The paper-based detection device exhibited a limit of detection (LOD) as few as 100 copies for antibiotic resistance genes. Meanwhile, it could detect antibiotic resistance genes from various bacteria. Noticeably, the approach can be applied to other genes besides antibiotic resistance genes by simply changing the LAMP primers. Therefore, this paper-based chip has the potential for point-of-care (POC) applications to detect various gene samples, especially in resource-limited conditions. | 2018 | 29323478 |
| 4761 | 15 | 0.9851 | Antimicrobial resistance and biofilm formation of penile prosthesis isolates: insights from in-vitro analysis. BACKGROUND: Inflatable penile prostheses (IPPs) have been shown to harbor biofilms in the presence and absence of infection despite exposure to various antimicrobials. Microbes persisting on IPPs following antibiotic exposure have not been adequately studied to assess biofilm formation capacity and antibiotic resistance. AIM: In this study, we aimed to assess these properties of microbes obtained from explanted infected and non-infected IPPS using an in vitro model. METHODS: 35 bacterial isolates were grown and tested against various single-agent or multiple agent antibiotic regimens including: bacitracin, cefaclor, cefazolin, gentamicin, levofloxacin, trimethoprim-sulfamethoxazole, tobramycin, vancomycin, piperacillin/tazobactam, gentamicin + piperacillin/tazobactam, gentamicin + cefazolin, and gentamicin + vancomycin. Zones of inhibition were averaged for each sample site and species. Statistics were analyzed with Holm's corrected, one-sample t-tests against a null hypothesis of 0. Isolates were also allowed to form biofilms in a 96-well polyvinyl plate and absorbance was tested at 570 nm using a microplate reader. OUTCOMES: Resistance was determined via clinical guidelines or previously established literature, and the mean and standard deviation of biofilm absorbance values were calculated and normalized to the optical density600 of the bacterial inoculum. RESULTS: Every species tested was able to form robust biofilms with the exception of Staphylococcus warneri. As expected, most bacteria were resistant to common perioperative antimicrobial prophylaxis. Gentamicin dual therapy demonstrated somewhat greater efficacy. STRENGTHS AND LIMITATIONS: This study examines a broad range of antimicrobials against clinically obtained bacterial isolates. However, not all species and antibiotics tested had standardized breakpoints, requiring the use of surrogate values from the literature. The microbes included in this study and their resistance genes are expectedly biased towards those that survived antibiotic exposure, and thus reflect the types of microbes which might "survive" in vivo exposure following revisional surgery. CLINICAL TRANSLATION: Despite exposure to antimicrobials, bacteria isolated during penile prosthesis revision for both infected and non-infected cases exhibit biofilm forming capacity and extensive antibiotic resistance patterns in vitro. These microbes merit further investigation to understand when simple colonization vs re-infection might occur. CONCLUSIONS: Although increasing evidence supports the concept that all IPPs harbor biofilms, even in the absence of infection, a deeper understanding of the characteristics of bacteria that survive revisional surgery is warranted. This study demonstrated extensive biofilm forming capabilities, and resistance patterns among bacteria isolated from both non-infected and infected IPP revision surgeries. Further investigation is warranted to determine why some devices become infected while others remain colonized but non-infected. | 2025 | 40062463 |
| 5825 | 16 | 0.9851 | Polymerase Chain Reaction (PCR) Profiling of Extensively Drug-Resistant (XDR) Pathogenic Bacteria in Pulmonary Tuberculosis Patients. Introduction Pulmonary tuberculosis (TB) remains a global health concern, exacerbated by the emergence of extensively drug-resistant (XDR) strains of Mycobacterium tuberculosis. This study employs advanced molecular techniques, specifically polymerase chain reaction (PCR) profiling, to comprehensively characterize the genetic landscape of XDR pathogenic bacteria in patients diagnosed with pulmonary TB. The objective of the study is to elucidate the genes that are associated with drug resistance in pulmonary TB strains through the application of PCR and analyze specific genetic loci that contribute to the development of resistance against multiple drugs. Materials and methods A total of 116 clinical samples suspected of TB were collected from the tertiary healthcare setting of Saveetha Medical College and Hospitals for the identification of MTB, which includes sputum (n = 35), nasal swabs (n = 17), blood (n = 44), and bronchoalveolar lavage (BAL) (n = 20). The collected specimens were processed and subjected to DNA extraction. As per the protocol, reconstitution of the DNA pellet was carried out. The reconstituted DNA was stored at -20 °C for the PCR assay. From the obtained positive sample specimens, XDR pulmonary TB specimens were focused on the targeted genes, specifically the rpoB gene for rifampicin resistance, inhA, and katG gene for thepromoter region for isoniazid resistance. Results Out of a total of 116 samples obtained, 53 tested positive for pulmonary TB, indicative of a mycobacterial infection. Among these positive cases, 43 patients underwent treatment at a tertiary healthcare facility. Subsequently, a PCR assay was performed with the extracted DNA for the target genes rpoB, inhA, and katG. Specifically, 22 sputum samples exhibited gene expression for rpoB, inhA, and katG, while nine nasal swabs showed expression of the rpoB and inhA genes. Additionally, rpoB gene expression was detected in seven blood specimens, and both rpoB and inhA genes were expressed in five BAL samples. Conclusion The swift diagnosis and efficient treatment of XDR-TB can be facilitated by employing advanced and rapid molecular tests and oral medication regimens. Utilizing both newly developed and repurposed anti-TB drugs like pretomanid, bedaquiline, linezolid, and ethionamide. Adhering to these current recommendations holds promise for managing XDR-TB effectively. Nevertheless, it is significant to conduct well-designed clinical trials and studies to further evaluate the efficacy of new agents and shorter treatment regimens, thus ensuring continuous improvement in the management of this challenging condition. | 2024 | 38953074 |
| 2599 | 17 | 0.9850 | Evaluation of whole-genome sequencing protocols for detection of antimicrobial resistance, virulence factors and mobile genetic elements in antimicrobial-resistant bacteria. Introduction. Antimicrobial resistance (AMR) poses a critical threat to global health, underscoring the need for rapid and accurate diagnostic tools. Methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae (ESBL-Kp) are listed among the World Health Organization's priority pathogens.Hypothesis. A rapid nanopore-based protocol can accurately and efficiently detect AMR genes, virulence factors (VFs) and mobile genetic elements (MGEs) in MRSA and ESBL-Kp, offering performance comparable to or superior to traditional sequencing methods.Aim. Evaluate whole-genome sequencing (WGS) protocols for detecting AMR genes, VFs and MGEs in MRSA and ESBL-Kp, to identify the most accurate and efficient tool for pathogen profiling.Methodology. Five distinct WGS protocols, including a rapid nanopore-based protocol (ONT20h) and four slower sequencing methods, were evaluated for their effectiveness in detecting genetic markers. The protocols' performances were compared across AMR genes, VFs and MGEs. Additionally, phenotypic antimicrobial susceptibility testing was performed to assess concordance with the genomic findings.Results. Compared to four slower sequencing protocols, the rapid nanopore-based protocol (ONT20h) demonstrated comparable or superior performance in AMR gene detection and equivalent VF identification. Although MGE detection varied among protocols, ONT20h showed a high level of agreement with phenotypic antimicrobial susceptibility testing.Conclusion. The findings highlight the potential of rapid WGS as a valuable tool for clinical microbiology, enabling timely implementation of infection control measures and informed therapeutic decisions. However, further studies are required to optimize the clinical application of this technology, considering costs, availability of bioinformatics tools and quality of reference databases. | 2025 | 40105741 |
| 5074 | 18 | 0.9850 | Cas14VIDet: A visual instant method free from PAM restriction for antibiotic resistance bacteria detection. A personalized treatment strategy that selects sensitive antibiotics based on Helicobacter pylori (H. pylori) resistance genes is currently the most effective approach to address the challenge of H. pylori eradication. However, the widespread adoption of this strategy is hindered by the long processing times and high costs associated with traditional resistance gene detection methods. In this study, we combined ultra-fast PCR with CRISPR/Cas14 into a single reaction system, establishing a rapid, one-pot visual platform named Cas14VIDet (Cas14-based Visual Instant Detection) for detecting H. pylori resistance genes. Cas14VIDet does not require a PAM sequence and excels in identifying single nucleotide polymorphisms, with the detection sensitivity approaching the level of a single bacterial colony (10(0) CFU/mL). The entire detection process can be completed within 10 min, and results are directly observable with the naked eye. We validated Cas14VIDet by testing 50 clinical samples and compared it with Sanger sequencing. The results showed that Cas14VIDet achieved 100% sensitivity, 100% specificity, and 100% accuracy in detecting H. pylori resistance genes to levofloxacin. Therefore, we believe this method holds great potential for rapid detection of H. pylori resistance, potentially supporting personalized treatment of H. pylori infections in the future. | 2025 | 39527901 |
| 5824 | 19 | 0.9850 | Evaluation of a micro/nanofluidic chip platform for the high-throughput detection of bacteria and their antibiotic resistance genes in post-neurosurgical meningitis. BACKGROUND: Post-neurosurgical meningitis (PNM) is one of the most severe hospital-acquired infections worldwide, and a large number of pathogens, especially those possessing multi-resistance genes, are related to these infections. Existing methods for detecting bacteria and measuring their response to antibiotics lack sensitivity and stability, and laboratory-based detection methods are inconvenient, requiring at least 24h to complete. Rapid identification of bacteria and the determination of their susceptibility to antibiotics are urgently needed, in order to combat the emergence of multi-resistant bacterial strains. METHODS: This study evaluated a novel, fast, and easy-to-use micro/nanofluidic chip platform (MNCP), which overcomes the difficulties of diagnosing bacterial infections in neurosurgery. This platform can identify 10 genus or species targets and 13 genetic resistance determinants within 1h, and it is very simple to operate. A total of 108 bacterium-containing cerebrospinal fluid (CSF) cultures were tested using the MNCP for the identification of bacteria and determinants of genetic resistance. The results were compared to those obtained with conventional identification and antimicrobial susceptibility testing methods. RESULTS: For the 108 CSF cultures, the concordance rate between the MNCP and the conventional identification method was 94.44%; six species attained 100% consistency. For the production of carbapenemase- and extended-spectrum beta-lactamase (ESBL)-related antibiotic resistance genes, both the sensitivity and specificity of the MNCP tests were high (>90.0%) and could fully meet the requirements of clinical diagnosis. CONCLUSIONS: The MNCP is fast, accurate, and easy to use, and has great clinical potential in the treatment of post-neurosurgical meningitis. | 2018 | 29559366 |